Editing Transfer RNA (section)

==tRNA biogenesis==
In [[eukaryotic]] cells, tRNAs are [[Transcription (genetics)|transcribed]] by [[RNA polymerase III]] as pre-tRNAs in the nucleus.<ref>{{cite journal | vauthors = White RJ | title = Regulation of RNA polymerases I and III by the retinoblastoma protein: a mechanism for growth control? | journal = Trends in Biochemical Sciences | volume = 22 | issue = 3 | pages = 77–80 | date = March 1997 | pmid = 9066256 | doi = 10.1016/S0968-0004(96)10067-0 }}</ref>
RNA polymerase III recognizes two highly conserved downstream promoter sequences: the 5′ intragenic control region (5′-ICR, D-control region, or A box), and the 3′-ICR (T-control region or B box) inside tRNA genes.<ref name="sharp1985" /><ref name="sharp1982">{{cite journal | vauthors = Sharp S, Dingermann T, Söll D | title = The minimum intragenic sequences required for promotion of eukaryotic tRNA gene transcription | journal = Nucleic Acids Research | volume = 10 | issue = 18 | pages = 5393–5406 | date = September 1982 | pmid = 6924209 | pmc = 320884 | doi = 10.1093/nar/10.18.5393 }}</ref><ref name="Dieci">{{cite journal | vauthors = Dieci G, Fiorino G, Castelnuovo M, Teichmann M, Pagano A | title = The expanding RNA polymerase III transcriptome | journal = Trends in Genetics | volume = 23 | issue = 12 | pages = 614–622 | date = December 2007 | pmid = 17977614 | doi = 10.1016/j.tig.2007.09.001 | hdl = 11381/1706964 | hdl-access = free }}</ref>
The first promoter begins at +8 of mature tRNAs and the second promoter is located 30–60 nucleotides downstream of the first promoter. The transcription terminates after a stretch of four or more [[thymidine]]s.<ref name="sharp1985" /><ref name="Dieci" />

[[File:Bulge-helix-bulge BHB tRNA intron.png|thumb|Bulge-helix-bulge motif of a tRNA intron]]
Pre-tRNAs undergo extensive modifications inside the nucleus. Some pre-tRNAs contain [[intron]]s that are spliced, or cut, to form the functional tRNA molecule;<ref>{{cite journal | vauthors = Tocchini-Valentini GD, Fruscoloni P, Tocchini-Valentini GP | title = Processing of multiple-intron-containing pretRNA | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 106 | issue = 48 | pages = 20246–20251 | date = December 2009 | pmid = 19910528 | pmc = 2787110 | doi = 10.1073/pnas.0911658106 | bibcode = 2009PNAS..10620246T | doi-access = free }}</ref> in bacteria these self-[[Splicing (genetics)|splice]], whereas in eukaryotes and [[archaea]] they are removed by tRNA-splicing [[endonuclease]]s.<ref>{{cite journal | vauthors = Abelson J, Trotta CR, Li H | title = tRNA splicing | journal = The Journal of Biological Chemistry | volume = 273 | issue = 21 | pages = 12685–12688 | date = May 1998 | pmid = 9582290 | doi = 10.1074/jbc.273.21.12685 | doi-access = free }}</ref> Eukaryotic pre-tRNA contains bulge-helix-bulge (BHB) structure motif that is important for recognition and precise splicing of tRNA intron by endonucleases.<ref name="Soma2014">{{cite journal | vauthors = Soma A | title = Circularly permuted tRNA genes: their expression and implications for their physiological relevance and development | journal = Frontiers in Genetics | volume = 5 | page = 63 | date = 2014 | pmid = 24744771 | pmc = 3978253 | doi = 10.3389/fgene.2014.00063 | doi-access = free }}</ref> This motif position and structure are evolutionarily conserved. However, some organisms, such as unicellular algae have a non-canonical position of BHB-motif as well as 5′- and 3′-ends of the spliced intron sequence.<ref name="Soma2014" />
The 5′ sequence is removed by [[RNase P]],<ref name="pmid9759486">{{cite journal | vauthors = Frank DN, Pace NR | title = Ribonuclease P: unity and diversity in a tRNA processing ribozyme | journal = Annual Review of Biochemistry | volume = 67 | issue = 1 | pages = 153–180 | year = 1998 | pmid = 9759486 | doi = 10.1146/annurev.biochem.67.1.153 | doi-access = free }}</ref> whereas the 3′ end is removed by the [[Ribonuclease Z|tRNase Z]] enzyme.<ref name="pmid17305600">{{cite journal | vauthors = Ceballos M, Vioque A | title = tRNase Z | journal = Protein and Peptide Letters | volume = 14 | issue = 2 | pages = 137–145 | year = 2007 | pmid = 17305600 | doi = 10.2174/092986607779816050 }}</ref>
A notable exception is in the [[archaeon]] ''[[Nanoarchaeum equitans]],'' which does not possess an RNase P enzyme and has a promoter placed such that transcription starts at the 5′ end of the mature tRNA.<ref name="pmid18451863">{{cite journal | vauthors = Randau L, Schröder I, Söll D | title = Life without RNase P | journal = Nature | volume = 453 | issue = 7191 | pages = 120–123 | date = May 2008 | pmid = 18451863 | doi = 10.1038/nature06833 | bibcode = 2008Natur.453..120R | s2cid = 3103527 }}</ref>
The non-templated 3′ CCA tail is added by a [[nucleotidyl transferase]].<ref name="pmid15498478">{{cite journal | vauthors = Weiner AM | title = tRNA maturation: RNA polymerization without a nucleic acid template | journal = Current Biology | volume = 14 | issue = 20 | pages = R883-5 | date = October 2004 | pmid = 15498478 | doi = 10.1016/j.cub.2004.09.069 | doi-access = free | bibcode = 2004CBio...14.R883W }}</ref>
Before tRNAs are [[Nuclear export|exported]] into the [[cytoplasm]] by Los1/[[Xpo-t]],<ref name="pmid9660920">{{cite journal | vauthors = Kutay U, Lipowsky G, Izaurralde E, Bischoff FR, Schwarzmaier P, Hartmann E, Görlich D | title = Identification of a tRNA-specific nuclear export receptor | journal = Molecular Cell | volume = 1 | issue = 3 | pages = 359–369 | date = February 1998 | pmid = 9660920 | doi = 10.1016/S1097-2765(00)80036-2 | doi-access = free }}</ref><ref name="pmid9512417">{{cite journal | vauthors = Arts GJ, Fornerod M, Mattaj IW | title = Identification of a nuclear export receptor for tRNA | journal = Current Biology | volume = 8 | issue = 6 | pages = 305–314 | date = March 1998 | pmid = 9512417 | doi = 10.1016/S0960-9822(98)70130-7 | s2cid = 17803674 | doi-access = free | bibcode = 1998CBio....8..305A }}</ref> tRNAs are [[aminoacylation|aminoacylated]].<ref name="pmid9857198">{{cite journal | vauthors = Arts GJ, Kuersten S, Romby P, Ehresmann B, Mattaj IW | title = The role of exportin-t in selective nuclear export of mature tRNAs | journal = The EMBO Journal | volume = 17 | issue = 24 | pages = 7430–7441 | date = December 1998 | pmid = 9857198 | pmc = 1171087 | doi = 10.1093/emboj/17.24.7430 }}</ref>
The order of the processing events is not conserved.
For example, in [[yeast]], the splicing is not carried out in the nucleus but at the cytoplasmic side of [[mitochondria]]l membranes.<ref name="pmid12925762">{{cite journal | vauthors = Yoshihisa T, Yunoki-Esaki K, Ohshima C, Tanaka N, Endo T | title = Possibility of cytoplasmic pre-tRNA splicing: the yeast tRNA splicing endonuclease mainly localizes on the mitochondria | journal = Molecular Biology of the Cell | volume = 14 | issue = 8 | pages = 3266–3279 | date = August 2003 | pmid = 12925762 | pmc = 181566 | doi = 10.1091/mbc.E02-11-0757 }}</ref>